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76 result(s) for "Geary, Peter"
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Biobanking for better healthcare
Translational cancer research is highly dependent of large series of cases including high quality samples and their associated data. Comprehensive Cancer Centers should be involved in networks to enable large-scale multi-center research projects between the centers [Ringborg, U., de Valeriola, D., van Harten, W., Llombart-Bosch, A., Lombardo, C., Nilsson, K., Philip, T., Pierotti, M.A., Riegman, P., Saghatchian, M., Storme, G., Tursz, T., Verellen, D, 2008. Improvement of European translational cancer research. Collaboration between comprehensive cancer centers. Tumori 94, 143–146.]. Combating cancer knows many frontiers. Research is needed for prevention as well as better care for those who have acquired the disease. This implies that human samples for cancer research need to be sourced from distinct forms of biobanking. An easier access to these samples for the scientific community is considered as the main bottleneck for research for health, and biobanks are the most adequate site to try to resolve this issue [Ozols, R.F., Herbst, R.S., Colson, Y.L., Gralow, J., Bonner, J., Curran Jr., W.J., Eisenberg, B.L., Ganz, P.A., Kramer, B.S., Kris, M.G., Markman, M., Mayer, R.J., Raghavan, D., Reaman, G.H., Sawaya, R., Schilsky, R.L., Schuchter, L.M., Sweetenham, J.W., Vahdat, L.T., Winn, R.J., and the American Society of Clinical Oncology, 2007. Clinical cancer advances 2006: major research advances in cancer treatment, prevention, and screening: a report from the American Society of Clinical Oncology. J. Clin. Oncol. 25, 146–162.]. However, biobanks should not be considered a static activity. On the contrary, biobanking is a young discipline [Morente, M.M., Fernandez, P.L., de Alava, E. Biobanking: old activity or young discipline? Semin. Diagn. Pathol., in press.], which need continuously evolve according to the permanent development of new techniques and new scientific goals. To accomplish current requirements of the scientific community biobanks need to face some essential challenges including an appropriate design, harmonized and more suitable procedures, and sustainability, all of them in the framework of their ethic, legal and social dimensions. This review therefore presents an overview on these issues, based on the works and discussions of the Marble Arch International Working Group on Biobanking for Biomedical Research, integrated by experts in biobanking from five continents.
Functional dissection of the conserved C. elegans LEM-3/ANKLE1 nuclease reveals a crucial requirement for the LEM-like and GIY-YIG domains for DNA bridges processing
Faithful chromosome segregation requires the removal of all DNA bridges physically linking chromatids before the completion of cell division. While several redundant safeguard mechanisms to process these DNA bridges exist from S-phase to late anaphase, the conserved LEM-3/ANKLE1 nuclease has been proposed to be part of a ‘last chance’ mechanism that acts at the midbody to eliminate DNA bridges that persist until late cytokinesis. We show that LEM-3 can cleave a wide range of branched DNA substrates, including flaps, forks, nicked and intact Holliday Junctions. AlphaFold modeling data suggest that the catalytic mechanism of LEM-3/ANKLE1 is conserved, mirroring the mechanism observed in bacterial GIY-YIG nucleases. We also present evidence that LEM-3 may form a homodimeric complex on the Holliday Junction DNA. LEM-3 DNA binding capacity requires both the LEM-like and the GIY-YIG nuclease domains; both are also essential for LEM-3 recruitment to the midbody and its nuclease activity. Finally, we show that preventing LEM-3 nuclear access is important to avoid toxicity, likely caused by branched DNAs cleavage during normal DNA metabolism. Our data suggest that C. elegans LEM-3 acts as a ‘last chance catch-all’ enzyme that processes DNA bridges caused by various perturbations of DNA metabolism just before cells divide.
The co-crystallisation of sugars by the supersaturation process
Co-crystallising sugars by the supersaturation process was investigated using sucrose and lactose as the matrix sugars. The components to be cocrystallised with either sucrose or lactose were a variety of mono- and disaccharides along with sweeteners such as saccharin. Analysis of the materials yielded from the supersaturation process was done primarily by differential scanning Calorimetry (DSC) and powder x-ray diffraction (PXRD). DSC analysis allowed information to be obtained on the thermal behaviour of the various co-crystalline materials, whilst PXRD permitted information on the structural aspects of the materials to be gained. These two forms of analysis were complimentary to each other, each revealed unique characteristics of the co-crystalline materials. To unambiguously differentiate the difference between a material that is co-crystalline and one that is not, physical blends of the sugars to be cocrystallised were analysed by DSC and PXRD. This approach allowed for identification of all the components in the mixture, more importantly, this identification was achievable at all levels of the second component in the mixture. Co-crystallising either sucrose or lactose, with various sugars, yielded solely co-crystalline material up to a certain level of the added sugar. Once this level has been reached, two distinct phases appear in both DSC and PXRD analysis. A co-crystallised and a phase relating to the added sugar can be observed. The formation of a potentially co-crystalline material appears to result from a direct inclusion of the added sugar into the matrix sugar. DSC analysis of the co-crystallised material revealed thermal behaviour that is suggestive of a doping of the matrix sugar by the added component. PXRD analysis did provide some data to further this argument, axis elongation for co-crystallised material is suggestive of a sopping of the main phase. However, determination of the unit cell volumes did not yield conclusive evidence to help prove this hypothesis though. This behaviour in both forms of analysis was generally proportional to the quantity of the second component that has become included into the matrix sugar. The formation of solely co-crystalline materials appears to rely on the structural similarity between the matrix sugar and the component to be included. A higher degree of similarity is reflected by a high level of inclusion of the added component. Co-crystallisation appears to rely on a degree of intermolecular sugar-sugar recognition. The inclusion of a second component is not solely down to structural similarities between materials however. It appears that there are kinetic factors potentially involved to. Varying the method of co-crystallisation allowed for higher, or lower, amounts of various second components to be included within a matrix sugar. The appearance of co-crystalline materials may be due to the inclusion of the second component in an amorphous state. Analysis by Autosorb of various co-crystalline materials has dispelled this idea. All co-crystalline materials behaved in a manner that was indicative of a crystalline material. During the course of the work with sucrose, it was noted that a unique melting point was observed. From previous work, this unique phase was thought to be a hydrated form of sucrose. Further analysis on this material has allowed for further postulation on its formation and on new methods of its synthesis.
Foreign exchange exposure in international corporations
This thesis investigates corporations that deal with foreign exchange exposure through the operations of its subsidiaries in foreign markets. The three categories of foreign exchange exposure, translation, transaction, and economic, as well as hedges, forward contracts, futures, options, and currency swaps, are all reviewed with appropriate examples. Existing policies of corporations that deal with foreign exchange exposure are divided between the different assumptions of the efficient market theory. These policies range from non-intervention to elaborate multi-faceted programs. The financial executives at seven corporations were personally interviewed. Their experiences and definitions are examined and recorded. The case studies of the corporations are divided into five sections; type of operations, structure, management attitude, nature of exposures, and hedging techniques. The conclusions reached by case analyses support the necessity of competitive hedges to excel in the inefficient world market. Therefore the validity of the efficient market theory, as it applies to international and domestic businesses, is questioned.
Uterine influences on conceptus development in fertility-classified animals
A major unresolved issue is how the uterus influences infertility and subfertility in cattle. Serial embryo transfer was previously used to classify heifers as high-fertile (HF), subfertile (SF), or infertile (IF). To assess pregnancy loss, two in vivo-produced embryos were transferred into HF, SF, and IF heifers on day 7, and pregnancy outcome was assessed on day 17. Pregnancy rate was substantially higher in HF (71%) and SF (90%) than IF (20%) heifers. Elongating conceptuses were about twofold longer in HF than SF heifers. Transcriptional profiling detected relatively few differences in the endometrium of nonpregnant HF, SF, and IF heifers. In contrast, there was a substantial difference in the transcriptome response of the endometrium to pregnancy between HF and SF heifers. Considerable deficiencies in pregnancy-dependent biological pathways associated with extracellular matrix structure and organization as well as cell adhesion were found in the endometrium of SF animals. Distinct gene expression differences were also observed in conceptuses from HF and SF animals, with many of the genes decreased in SF conceptuses known to be embryonic lethal in mice due to defects in embryo and/or placental development. Analyses of biological pathways, key players, and ligand–receptor interactions based on transcriptome data divulged substantial evidence for dysregulation of conceptus–endometrial interactions in SF animals. These results support the ideas that the uterus impacts conceptus survival and programs conceptus development, and ripple effects of dysregulated conceptus–endometrial interactions elicit loss of the postelongation conceptus in SF cattle during the implantation period of pregnancy.
Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle
Infertility and subfertility negatively impact the economics and reproductive performance of cattle. Of note, significant pregnancy loss occurs in cattle during the first month of pregnancy, yet little is known about the genetic loci influencing pregnancy success and loss in cattle. To identify quantitative trait loci (QTL) with large effects associated with early pregnancy loss, Angus crossbred heifers were classified based on day 28 pregnancy outcomes to serial embryo transfer. A genome wide association analysis (GWAA) was conducted comparing 30 high fertility heifers with 100% success in establishing pregnancy to 55 subfertile heifers with 25% or less success. A gene set enrichment analysis SNP (GSEA-SNP) was performed to identify gene sets and leading edge genes influencing pregnancy loss. The GWAA identified 22 QTL (p < 1 x 10-5), and GSEA-SNP identified 9 gene sets (normalized enrichment score > 3.0) with 253 leading edge genes. Network analysis identified TNF (tumor necrosis factor), estrogen, and TP53 (tumor protein 53) as the top of 671 upstream regulators (p < 0.001), whereas the SOX2 (SRY [sex determining region Y]-box 2) and OCT4 (octamer-binding transcription factor 4) complex was the top master regulator out of 773 master regulators associated with fertility (p < 0.001). Identification of QTL and genes in pathways that improve early pregnancy success provides critical information for genomic selection to increase fertility in cattle. The identified genes and regulators also provide insight into the complex biological mechanisms underlying pregnancy establishment in cattle.
Drivers of density and sex ratio in the leopard Panthera pardus population of Hluhluwe-iMfolozi Park, South Africa
The leopard Panthera pardus is a widespread felid, distributed throughout Africa, Asia and parts of the Middle East. The survival of the African leopard Panthera pardus pardus is significantly higher within protected areas but numerous factors influence the growth and stability of populations. Monitoring population density and demographics over a long timeframe can help to identify the drivers of change and inform conservation actions. We aimed to determine the drivers of change in leopard populations in a protected area and to identify those factors that encourage leopards to remain within the reserve, so that appropriate conservation management actions can be implemented to improve leopard survival and reduce human–wildlife conflict. We used camera trapping to monitor changes in the leopard population in Hluhluwe-iMfolozi Park, South Africa, in a long-term study during 2013–2022. We applied spatially explicit capture–recapture models to the camera-trap data to determine annual population density and sex ratio. We estimated that leopard density declined from six to four individuals per 100 km2 over the study decade. The sex ratio was heavily female-biased during the first years of the study but was male-biased by 2022 (male : female ratio of 0.64 : 0.36). Individual leopards remained in the Park for 2.45 years on average and annual turnover was high. The abundance of other predators and the level of conflict with people affected leopard density and their duration of residency in the Park, and annual rainfall also had an effect. Instability within leopard populations affects population growth and is linked to a range of factors such as prey availability, habitat fragmentation and persecution. However, immigration of males from other populations should increase genetic diversity and improve breeding success. Understanding the drivers of leopard population dynamics, and the factors that cause them to remain inside protected areas, can help with the design and implementation of appropriate conservation management actions to lower individual turnover and limit human–wildlife conflict.
A Comprehensive Analysis of Common Genetic Variation Around Six Candidate Loci for Intrahepatic Cholestasis of Pregnancy
Intrahepatic cholestasis of pregnancy (ICP) has a complex etiology with a significant genetic component. Heterozygous mutations of canalicular transporters occur in a subset of ICP cases and a population susceptibility allele (p.444A) has been identified in ABCB11. We sought to expand our knowledge of the detailed genetic contribution to ICP by investigation of common variation around candidate loci with biological plausibility for a role in ICP (ABCB4, ABCB11, ABCC2, ATP8B1, NR1H4, and FGF19). ICP patients (n=563) of white western European origin and controls (n=642) were analyzed in a case-control design. Single-nucleotide polymorphism (SNP) markers (n=83) were selected from the HapMap data set (Tagger, Haploview 4.1 (build 22)). Genotyping was performed by allelic discrimination assay on a robotic platform. Following quality control, SNP data were analyzed by Armitage's trend test. Cochran-Armitage trend testing identified six SNPs in ABCB11 together with six SNPs in ABCB4 that showed significant evidence of association. The minimum Bonferroni corrected P value for trend testing ABCB11 was 5.81×10(-4) (rs3815676) and for ABCB4 it was 4.6×10(-7)(rs2109505). Conditional analysis of the two clusters of association signals suggested a single signal in ABCB4 but evidence for two independent signals in ABCB11. To confirm these findings, a second study was performed in a further 227 cases, which confirmed and strengthened the original findings. Our analysis of a large cohort of ICP cases has identified a key role for common variation around the ABCB4 and ABCB11 loci, identified the core associations, and expanded our knowledge of ICP susceptibility.
Kepler-47: A Transiting Circumbinary Multiplanet System
We report the detection of Kepler-47, a system consisting of two planets orbiting around an eclipsing pair of stars. The inner and outer planets have radii 3.0 and 4.6 times that of Earth, respectively. The binary star consists of a Sun-like star and a companion roughly one-third its size, orbiting each other every 7.45 days. With an orbital period of 49.5 days, 18 transits of the inner planet have been observed, allowing a detailed characterization of its orbit and those of the stars. The outer planet's orbital period is 303.2 days, and although the planet is not Earth-like, it resides within the classical \"habitable zone,\" where liquid water could exist on an Earth-like planet. With its two known planets, Kepler-47 establishes that close binary stars can host complete planetary systems.
How Micronutrient Status May Affect Eating Behavior—Hypothesis and Perspectives
The importance of micronutrient status in human food choice remains a fundamental issue needing further investigation. The objectives of the present paper are to present and discuss historic and current research together with a general model incorporating this interaction and to suggest future research to address the questions this poses. By definition, essential nutrients must be consumed in sufficient amounts to meet an individual’s requirements. While data indicate that complex neuroendocrine mechanisms provide negative-feedback control of energy and protein intake to support homeostasis, corresponding mechanisms controlling micronutrient intake are less well studied. In some contexts, they are explicitly assumed to be absent, specifically for models evaluating safety and risks of deficiencies. However, it may be hypothesized that for at least some micronutrients, mechanisms exist that aid attainment of requirements by altering preference for micronutrient-rich foods so as to increase ingestion of foods containing them, similar to how being thirsty increases the appeal of watermelon compared with dry food. If this hypothesis is correct, it may hold important implications for understanding the types and quantities of foods ingested. Greater appeal in foods richer in essential nutrients may reduce the risk of malnutrition. However, by extension, it may be posited that the use of supplements could confound the most healthful food choices. For example, obtaining vitamin C from supplements or fortified foods could then causally reduce the dietary intake of vegetables and fruits by reducing the appeal of these foods. The unintended consequence may be a lower intake of fiber, nitrate, and phytochemicals, food constituents that may contribute to health without being essential nutrients themselves. This hypothesis can and should be tested empirically, for example, through randomized placebo-controlled supplementation trials. If clear causal effects are documented, clinical and public health guidance will require critical evaluation and possible modification.